NEW: We changed the default behavior of save_tmp (now False). Pass --save_tmp for retrocompatibility
NEW: We changed the default beavior of save_panda_results. Now all PANDA outputs have column headers by default. Pass old_compatible for the previous behavior
Input data:
Expression: tcga_coad_cms3.nodot.txt
Motif data: /home/ubuntu/tcga-coad-subtype/priors/MotifPriorGencode_p5.txt
PPI data: /home/ubuntu/tcga-coad-subtype/priors/ppi_Gencode_p5.txt
Start Panda run ...
Loading motif data ...
  Elapsed time: 2.84 sec.
Loading expression data ...
  Elapsed time: 0.22 sec.
Loading PPI data ...
Number of PPIs: 138479
  Elapsed time: 0.05 sec.
Calculating coexpression network ...
  Elapsed time: 4.15 sec.
Creating motif network ...
  Elapsed time: 3.59 sec.
Creating PPI network ...
  Elapsed time: 0.11 sec.
intersection /home/ubuntu/tcga-coad-subtype/priors/MotifPriorGencode_p5.txt tcga_coad_cms3.nodot.txt /home/ubuntu/tcga-coad-subtype/priors/ppi_Gencode_p5.txt False False False
Normalizing networks ...
  Elapsed time: 23.56 sec.
Running PANDA algorithm ...
Computing panda on CPU
step: 0, hamming: 2.4797399450024997
step: 1, hamming: 0.5613464171356649
step: 2, hamming: 0.4328668442276429
step: 3, hamming: 0.3803424324842699
step: 4, hamming: 0.3431463078821702
step: 5, hamming: 0.31034423965725827
step: 6, hamming: 0.27930682625217884
step: 7, hamming: 0.24956579398032488
step: 8, hamming: 0.22128289618700114
step: 9, hamming: 0.1947525527989249
step: 10, hamming: 0.17022737410235209
step: 11, hamming: 0.1478645625230561
step: 12, hamming: 0.12772161269564308
step: 13, hamming: 0.10977132955631987
step: 14, hamming: 0.09392267765283399
step: 15, hamming: 0.08004158978476388
step: 16, hamming: 0.06796827736220241
step: 17, hamming: 0.057530804819989095
step: 18, hamming: 0.04855527766713414
step: 19, hamming: 0.04087286375936921
step: 20, hamming: 0.03432434526445315
step: 21, hamming: 0.02876280738827118
step: 22, hamming: 0.024054963882954916
step: 23, hamming: 0.02008149562563979
step: 24, hamming: 0.016736753307733897
step: 25, hamming: 0.013928025806894551
step: 26, hamming: 0.011574570732390656
step: 27, hamming: 0.00960652167269605
step: 28, hamming: 0.007963760112403143
step: 29, hamming: 0.006594805645328073
step: 30, hamming: 0.005455762812737385
step: 31, hamming: 0.004509345204973599
step: 32, hamming: 0.0037239875643362828
step: 33, hamming: 0.003073048982238789
step: 34, hamming: 0.0025341061946588346
step: 35, hamming: 0.002088332728013777
step: 36, hamming: 0.0017199574609727802
step: 37, hamming: 0.0014157958872150335
step: 38, hamming: 0.0011648463636391394
step: 39, hamming: 0.0009579443679928416
Running panda took: 649.51 seconds!
Saving PANDA network to panda_tcga_coad_cms3.txt ...
WARNING: panda is now saved with the column names. 
Use old_compatible=True to save the panda results as previous versions without header
  Elapsed time: 43.52 sec.
